Applying a force to a molecule in water

From: Monika Madhavi (
Date: Sat Jan 01 2022 - 00:54:40 CST

Dear all,

I have a protein in a water box as my system and want to translate my
protein inside the water box. I tried applying a constant force to all
protein atoms as given in the "user defined forces" tutorial. Without
water, the protein translates as I want but when I add water it gives the
following errors and does not create the output.

ERROR: Constraint failure in RATTLE algorithm for atom 65!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on
patch 19 pe 4)

I would be grateful if you can explain the reason for these errors and what
is the standard method to apply a force to a molecule through water.

Thank you.

W.A.Monika Madhavi
Senior Lecturer,
Department of Physics,
University of Colombo.

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